Controversial emergency surveillance legislation has cleared the Commons after an extended sitting and angry exchanges alleging an abuse of parliament.

A hard core of up to 56 MPs opposed the deal between the three main parties after the frontbenches agreed on the urgent need for new laws.

The data retention and investigatory powers bill was agreed at third reading by an overwhelming majority of 416, after MPs voted 449 to 33 in favour.

Earlier, Labour MP Tom Watson's cross-party bid to force the legislation to expire by the end of the year was defeated 454 vote to 56, majority 398.

The government did concede additional reviews of investigatory regulations – both a general review at ministers' own initiative to be completed by the election and six-monthly reviews of the bill proposed by Labour.

The House of Lords will look at the bill on Wednesday and Thursday as ministers aim to have it sent for royal assent before the end of the week.

Backbenchers across the Commons complained bitterly at the prospect of the bill being forced through in a day.

Former Tory leadership contender David Davis said: "My understanding is there was an argument inside government between the two halves of the coalition and that argument has gone on for three months so what the coalition cannot decide in three months this house has to decide in one day."

Veteran Labour MP David Winnick, a member of the home affairs select committee, said: "I consider this to be an outright abuse of parliamentary procedure."

The home secretary, Theresa May, defended the bill as a narrow set of proposals vital for national security and public safety in the wake of a European court of justice ruling in April.

The government has insisted the ruling throws into doubt existing regulations, meaning communications companies could begin deleting vital data. Ministers claim the bill only reinforces the status quo and does not create new powers.

May warned: "If we delay we face the appalling prospect police operations will go dark, that trails will go cold, that terrorist plots will go undetected.

"If that happens, innocent lives may be lost."

The shadow home secretary, Yvette Cooper, said Labour would support the "sticking plaster" bill but insisted it had to be the beginning of a much wider debate on safety versus civil liberties.

She told the house: "The home secretary will recognise that parliament has been put in a difficult position by this emergency legislation this week.

"This is not the way that this kind of legislation should be done. Let's be clear, the last-minute nature of it does undermine trust in the government's intentions but also in the vital work the police and agencies need to do.

"But I also have no doubt this legislation is needed and that we cannot delay it until the autumn."